SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_8_s1_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_8_s1_R2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 498.04 s (17 us/read; 3.57 M reads/minute). === Summary === Total reads processed: 29,619,538 Reads with adapters: 10,646,858 (35.9%) Reads written (passing filters): 29,619,538 (100.0%) Total basepairs processed: 2,266,654,553 bp Quality-trimmed: 1,200,478 bp (0.1%) Total written (filtered): 2,253,454,035 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10646858 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.1% C: 14.5% G: 3.5% T: 35.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10020563 7404884.5 0 10020563 2 428579 1851221.1 0 428579 3 127057 462805.3 0 127057 4 25733 115701.3 0 25733 5 2192 28925.3 0 2192 6 2101 7231.3 0 2101 7 447 1807.8 0 447 8 226 452.0 0 226 9 1258 113.0 0 1038 220 10 1006 28.2 1 132 874 11 1561 7.1 1 579 982 12 1584 1.8 1 213 1371 13 2970 0.4 1 0 2970 14 5029 0.4 1 0 5029 15 8015 0.4 1 0 8015 16 10482 0.4 1 0 10482 17 6434 0.4 1 0 6434 18 502 0.4 1 0 502 19 89 0.4 1 0 89 20 69 0.4 1 0 69 21 33 0.4 1 0 33 22 35 0.4 1 0 35 23 53 0.4 1 0 53 24 55 0.4 1 0 55 25 51 0.4 1 0 51 26 43 0.4 1 0 43 27 39 0.4 1 0 39 28 34 0.4 1 0 34 29 42 0.4 1 0 42 30 42 0.4 1 0 42 31 41 0.4 1 0 41 32 48 0.4 1 0 48 33 37 0.4 1 0 37 34 25 0.4 1 0 25 35 21 0.4 1 0 21 36 24 0.4 1 0 24 37 14 0.4 1 0 14 38 20 0.4 1 0 20 39 15 0.4 1 0 15 40 18 0.4 1 0 18 41 15 0.4 1 0 15 42 14 0.4 1 0 14 43 23 0.4 1 0 23 44 15 0.4 1 0 15 45 14 0.4 1 0 14 46 15 0.4 1 0 15 47 11 0.4 1 0 11 48 19 0.4 1 0 19 49 12 0.4 1 0 12 50 21 0.4 1 0 21 51 13 0.4 1 0 13 52 6 0.4 1 0 6 53 4 0.4 1 0 4 54 11 0.4 1 0 11 55 8 0.4 1 0 8 56 6 0.4 1 0 6 57 8 0.4 1 0 8 58 13 0.4 1 0 13 59 5 0.4 1 0 5 60 7 0.4 1 0 7 61 3 0.4 1 0 3 62 3 0.4 1 0 3 63 4 0.4 1 0 4 64 2 0.4 1 0 2 65 3 0.4 1 0 3 66 1 0.4 1 0 1 67 4 0.4 1 0 4 68 2 0.4 1 0 2 69 1 0.4 1 0 1 70 3 0.4 1 0 3 72 3 0.4 1 0 3 73 2 0.4 1 0 2 RUN STATISTICS FOR INPUT FILE: zr2096_8_s1_R2_val_2.fq.gz ============================================= 29619538 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 29619538 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 93858 (0.32%)